1) I used nuclear reactions just as a fill in to say it should be possible to simulate matter with close enough approximation to facilitate thought. This was posited in "A New Kind of Math" which suggests there is a thing as "computation equivalence", which is a theory I mostly subscribe to. If we wanted to simulate a human naively, we would probably only care about biochemical reactions at earth like temps, not nuclear or quantum physics.

2) I’m not sure matrix math is sufficient, but let’s ignore that because I feel some kind of math is sufficient, and any computer program will have the same question apply. I also feel the universe might be the most efficient computer in time and space, which means we aren’t living in a simulation, because the computer would be bigger and run time slower than the reality it simulates.

- I don’t think it matters where the network is in reality. Virtual is fine. In a mostly perfect simulation of reality (let say enough to accurately model biochemical processes), there will be some state of the program, and for something living in the simulation, they will feel alive if they are complex enough.

They will experience time differently than we do, but they will arrive at their own conclusions as part of the simulation.